If I'm flatting a particular flop it's because I'm generally trying to balance with the rest of my range on a particular board.

If I have 89dd on Jx5d2d, I may flat this flop because most of my range (88,99,TT,Jx) will be flatting this flop. Raising this flop is very polarized to either 222/555 or a FD and given the number of combos of FD's to sets, it really weights our range to FD's if we raise.

By contrast, if I flat 88-TT,Jx and face a turn check. I will often be betting these hands. Since I'm betting these hands I can also bet my FD's on the turn. Calling the flop with a FD does not need to equate to checking back turn with a FD at all. They are completely separate actions. Also very few people take bet turn + c/r turn lines much anymore, so there's less risk getting blown off the draw if you bet.